chr16-28618867-T-C

Variant names:

• chr16-28618867-T-C
• rs7192559
• ENST00000562058.5:n.494+1196A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394421.1(SULT1A1):​c.-339+1196A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 152,234 control chromosomes in the GnomAD database, including 64,209 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.91 (64209 hom., cov: 32)
• Consequence: SULT1A1 NM_001394421.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

ENSG00000289755 (HGNC:):

SULT1A1 (HGNC:11453): (sulfotransferase family 1A member 1) Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These cytosolic enzymes are different in their tissue distributions and substrate specificities. The gene structure (number and length of exons) is similar among family members. This gene encodes one of two phenol sulfotransferases with thermostable enzyme activity. Multiple alternatively spliced variants that encode two isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT1A1	NM_001394421.1	c.-339+1196A>G		intron_variant	Intron 2 of 10		NP_001381350.1
SULT1A1	NM_001394422.1	c.-1138+1196A>G		intron_variant	Intron 2 of 9		NP_001381351.1
SULT1A1	NM_001394423.1	c.-469+1196A>G		intron_variant	Intron 2 of 11		NP_001381352.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289755	ENST00000562058.5	n.494+1196A>G		intron_variant	Intron 2 of 9	1
ENSG00000289755	ENST00000564818.5	n.193+1196A>G		intron_variant	Intron 2 of 10	1
ENSG00000289755	ENST00000563493.1	n.566+1196A>G		intron_variant	Intron 2 of 8	5

Frequencies

GnomAD3 genomes AF: 0.908 AC: 138046 AN: 152116 Hom.: 64179 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.935

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.907 AC: 138131 AN: 152234 Hom.: 64209 Cov.: 32 AF XY: 0.912 AC XY: 67917 AN XY: 74430

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.962

Gnomad4 ASJ AF: 0.991

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.999

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.999

Gnomad4 OTH AF: 0.936

Alfa AF: 0.977 Hom.: 80447

Bravo AF: 0.895

Asia WGS AF: 0.979 AC: 3405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7192559; hg19: chr16-28630188;